Sample-level analysis

These tutorials focus on the preprocessing, analysis and handling of individual samples of single-cell spatial transcriptomics data. These notebooks can be run from top to bottom and require the notebook about automated image registration to be run first.

First analysis steps

Tutorial with introduction into first steps of analysis including filtering, preprocessing and dimensionality reduction.

Data preprocessing and analysis

Annotations in InSituPy

Tutorial introducing how to import annotations and regions from external sources like QuPath or add them in the napari viewer.

Working with histological annotations and regions

Crop data

Tutorial showing how to crop data.

Cropping the data

Cell type annotation

Tutorial showing different options to perform cell type annotation.

Cell type annotation

Explore gene expression along an axis

Demonstration on how to explore gene expression along an axis of the dataset.

Investigate gene expression and cell density along an axis

Build an InSituData object from scratch

Tutorial on how to generate an InSituData object from scratch.

Build an InSituData object from scratch

Perform segmentation with Proseg and add the results to InSituData

Tutorial on how to improve cell segmentation with Proseg and add the data to InSituData for downstream analysis.

Notebook demonstrating the addition of data segmented with proseg